BUG
The Web Mercator projected coordinate system isn't appropriate for measuring planar distances and areas. If a map or a local scene uses Web Mercator, it would be necessary to measure distances and areas as geodesic and not planar.
Unfortunately, measuring the geodesic distance with the Measure tool in ArcGIS Pro does not work in a local scene which uses Web Mercator Auxiliary Sphere (EPSG: 3857).
The screenshot below shows the measuring result for a 500m cube which was collected in Web Mercator. The geodesic distance should be significantly smaller than 500 m.

However measuring the geodesic distance in a map that uses Web Mercator does work as expected, as shown in the next image.

This is a known issue, BUG-000172263: ArcGIS Pro - Measuring geodesic distance does not work as expected in local scenes with Projected Coordinate System Web Mercator Auxiliary Sphere (EPSG code: 3857).
Change the coordinate system for the local scene from Web Mercator Auxiliary Sphere to a more appropriate projected coordinate system such as UTM, as shown in the image below.

Measuring the geodesic distance should now work as expected.

Article ID: 000034189
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